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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375180	XR_007060245.1	n.460+9444T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223838	ENST00000779057.1	n.135+40106T>C		intron_variant	Intron 1 of 1
ENSG00000223838	ENST00000779058.1	n.428-3152T>C		intron_variant	Intron 4 of 4
ENSG00000223838	ENST00000779059.1	n.523-3152T>C		intron_variant	Intron 5 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs2892937; hg19: chr7-19658389;