1-77272697-G-T

Variant names:

• chr1-77272697-G-T
• rs10493537
• ENST00000810814.1:n.101+10336C>A

Variant summary

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

The ENST00000810814.1(ENSG00000305415):​n.101+10336C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 152,240 control chromosomes in the GnomAD database, including 327 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 0.054 (327 hom., cov: 33)
• Consequence: ENSG00000305415 ENST00000810814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 2 publications found

Genes affected

ENSG00000305415 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

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
ENSG00000305415	ENST00000810814.1	n.101+10336C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8265 AN: 152122 Hom.: 320 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0544 AC: 8288 AN: 152240 Hom.: 327 Cov.: 33 AF XY: 0.0575 AC XY: 4282 AN XY: 74436

African (AFR) AF: 0.0576 AC: 2391 AN: 41532

American (AMR) AF: 0.0597 AC: 913 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.170 AC: 881 AN: 5188

South Asian (SAS) AF: 0.192 AC: 925 AN: 4814

European-Finnish (FIN) AF: 0.0491 AC: 520 AN: 10598

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2375 AN: 68026

Other (OTH) AF: 0.0605 AC: 128 AN: 2114

Alfa AF: 0.0461 Hom.: 28

Bravo AF: 0.0536

Asia WGS AF: 0.208 AC: 724 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	0.088
DANN	Benign	0.40
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10493537; hg19: chr1-77738382;