rs2892937

Variant names:

• chr7-19618766-T-C
• rs2892937
• ENST00000779057.1:n.135+40106T>C

Variant summary

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

The ENST00000779057.1(ENSG00000223838):​n.135+40106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,208 control chromosomes in the GnomAD database, including 228 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 0.048 (228 hom., cov: 31)
• Consequence: ENSG00000223838 ENST00000779057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 3 publications found

Genes affected

ENSG00000223838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779057.1. 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
	ENSG00000223838	ENST00000779057.1		n.135+40106T>C		intron	N/A
	ENSG00000223838	ENST00000779058.1		n.428-3152T>C		intron	N/A
	ENSG00000223838	ENST00000779059.1		n.523-3152T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7312 AN: 152090 Hom.: 228 Cov.: 31

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0445

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0480 AC: 7312 AN: 152208 Hom.: 228 Cov.: 31 AF XY: 0.0495 AC XY: 3685 AN XY: 74418

African (AFR) AF: 0.0324 AC: 1348 AN: 41558

American (AMR) AF: 0.0300 AC: 458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.122 AC: 632 AN: 5174

South Asian (SAS) AF: 0.0798 AC: 385 AN: 4824

European-Finnish (FIN) AF: 0.0604 AC: 640 AN: 10588

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0521 AC: 3546 AN: 68006

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0513 Hom.: 375

Bravo AF: 0.0447

Asia WGS AF: 0.116 AC: 400 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		0.27

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: rs2892937;

hg19: chr7-19658389;