rs76387818

Variant names:

• chr1-97073844-G-A
• rs76387818
• ENST00000737657.1:n.550-7903G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000737657.1(ENSG00000296260):​n.550-7903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,206 control chromosomes in the GnomAD database, including 44 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 0.022 (44 hom., cov: 32)
• Consequence: ENSG00000296260 ENST00000737657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 11 publications found

Genes affected

ENSG00000296260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.022 (3344/152206) while in subpopulation NFE AF = 0.0324 (2202/67990). AF 95% confidence interval is 0.0313. There are 44 homozygotes in GnomAd4. There are 1551 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296260	ENST00000737657.1	n.550-7903G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3347 AN: 152088 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00975

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0220 AC: 3344 AN: 152206 Hom.: 44 Cov.: 32 AF XY: 0.0208 AC XY: 1551 AN XY: 74406

African (AFR) AF: 0.00970 AC: 403 AN: 41556

American (AMR) AF: 0.0218 AC: 333 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4824

European-Finnish (FIN) AF: 0.0228 AC: 242 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2202 AN: 67990

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0279 Hom.: 101

Bravo AF: 0.0218

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs76387818; hg19: chr1-97539400;