rs2240571

Variant names:

• chr7-12570362-G-C
• rs2240571
• ENST00000433040.1:n.674C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766149.1(ENSG00000225606):​n.700C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 227,950 control chromosomes in the GnomAD database, including 32,570 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (22448 hom., cov: 33)
  • Exomes 𝑓: 0.50 (10122 hom.)
• Consequence: ENSG00000225606 ENST00000766149.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 8 publications found

Genes affected

ENSG00000225606 (HGNC:):

SCIN (HGNC:21695): (scinderin) SCIN is a Ca(2+)-dependent actin-severing and -capping protein (Zunino et al., 2001 [PubMed 11568009]).[supplied by OMIM, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766149.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225606	ENST00000433040.1	TSL:5	n.674C>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000225606	ENST00000766149.1		n.700C>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000225606	ENST00000766153.1		n.1293C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81785 AN: 151960 Hom.: 22419 Cov.: 33

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.501 AC: 38043 AN: 75870 Hom.: 10122 Cov.: 0 AF XY: 0.507 AC XY: 20920 AN XY: 41278

African (AFR) AF: 0.600 AC: 969 AN: 1614

American (AMR) AF: 0.425 AC: 1035 AN: 2438

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 878 AN: 1802

East Asian (EAS) AF: 0.358 AC: 717 AN: 2000

South Asian (SAS) AF: 0.537 AC: 7652 AN: 14238

European-Finnish (FIN) AF: 0.475 AC: 2346 AN: 4936

Middle Eastern (MID) AF: 0.649 AC: 1165 AN: 1794

European-Non Finnish (NFE) AF: 0.496 AC: 21328 AN: 42980

Other (OTH) AF: 0.480 AC: 1953 AN: 4068

GnomAD4 genome AF: 0.538 AC: 81858 AN: 152080 Hom.: 22448 Cov.: 33 AF XY: 0.535 AC XY: 39748 AN XY: 74348

African (AFR) AF: 0.630 AC: 26131 AN: 41472

American (AMR) AF: 0.465 AC: 7112 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1933 AN: 5156

South Asian (SAS) AF: 0.548 AC: 2643 AN: 4820

European-Finnish (FIN) AF: 0.485 AC: 5122 AN: 10568

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35247 AN: 67984

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.533 Hom.: 2679

Bravo AF: 0.537

Asia WGS AF: 0.462 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.71
PhyloP100		-0.063
PromoterAI		0.078	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2240571;

hg19: chr7-12609988;

COSMIC: COSV107380717;