chr7-113806501-G-A

Variant names:

• chr7-113806501-G-A
• rs989613

Variant summary

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

The variant allele was found at a frequency of 0.194 in 151,662 control chromosomes in the GnomAD database, including 3,168 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 0.19 (3168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29451 AN: 151552 Hom.: 3153 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.194 AC: 29492 AN: 151662 Hom.: 3168 Cov.: 31 AF XY: 0.195 AC XY: 14451 AN XY: 74090

African (AFR) AF: 0.181 AC: 7500 AN: 41416

American (AMR) AF: 0.325 AC: 4934 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1424 AN: 5130

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4804

European-Finnish (FIN) AF: 0.120 AC: 1265 AN: 10502

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12250 AN: 67868

Other (OTH) AF: 0.182 AC: 382 AN: 2098

Alfa AF: 0.185 Hom.: 1765

Bravo AF: 0.207

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.6
DANN	Benign	0.62
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs989613; hg19: chr7-113446556;