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 ENST00000433040.1(ENSG00000225606):​n.674C>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 ENST00000433040.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986768	XR_007060635.1	n.1866C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225606	ENST00000433040.1	n.674C>G		non_coding_transcript_exon_variant	Exon 2 of 2	5
ENSG00000225606	ENST00000766149.1	n.700C>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000225606	ENST00000766153.1	n.1293C>G		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2240571; hg19: chr7-12609988; COSMIC: COSV107380717;