rs117982730

Variant names:

• chr7-126256694-G-A
• rs117982730
• ENST00000809641.1:n.220+23082G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-126256694-G-A
• chr7-126256694-G-T

Variant summary

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

The ENST00000809641.1(ENSG00000305210):​n.220+23082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 152,056 control chromosomes in the GnomAD database, including 39 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 0.018 (39 hom., cov: 32)
• Consequence: ENSG00000305210 ENST00000809641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 0 publications found

Genes affected

ENSG00000305210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0176 (2677/152056) while in subpopulation NFE AF = 0.0257 (1746/67968). AF 95% confidence interval is 0.0247. There are 39 homozygotes in GnomAd4. There are 1299 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 39 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
ENSG00000305210	ENST00000809641.1	n.220+23082G>A		intron_variant	Intron 2 of 2
ENSG00000305210	ENST00000809642.1	n.202+23082G>A		intron_variant	Intron 2 of 2
ENSG00000305210	ENST00000809643.1	n.269+23082G>A		intron_variant	Intron 2 of 2
ENSG00000305210	ENST00000809644.1	n.222+22811G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2676 AN: 151938 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.00329

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00477

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0176 AC: 2677 AN: 152056 Hom.: 39 Cov.: 32 AF XY: 0.0175 AC XY: 1299 AN XY: 74326

African (AFR) AF: 0.00328 AC: 136 AN: 41486

American (AMR) AF: 0.0115 AC: 176 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5154

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4822

European-Finnish (FIN) AF: 0.0406 AC: 429 AN: 10568

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0257 AC: 1746 AN: 67968

Other (OTH) AF: 0.0180 AC: 38 AN: 2106

Alfa AF: 0.0220 Hom.: 56

Bravo AF: 0.0139

Asia WGS AF: 0.00318 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.31
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs117982730; hg19: chr7-125896748;