chr7-68694605-G-T

Variant names:

• chr7-68694605-G-T
• rs723886

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 0.397 in 151,858 control chromosomes in the GnomAD database, including 12,937 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 0.40 (12937 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.397 AC: 60182 AN: 151742 Hom.: 12909 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.397 AC: 60257 AN: 151858 Hom.: 12937 Cov.: 32 AF XY: 0.393 AC XY: 29137 AN XY: 74210

African (AFR) AF: 0.568 AC: 23484 AN: 41374

American (AMR) AF: 0.308 AC: 4691 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1142 AN: 3460

East Asian (EAS) AF: 0.379 AC: 1959 AN: 5164

South Asian (SAS) AF: 0.400 AC: 1921 AN: 4806

European-Finnish (FIN) AF: 0.329 AC: 3466 AN: 10536

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22346 AN: 67958

Other (OTH) AF: 0.401 AC: 846 AN: 2108

Alfa AF: 0.321 Hom.: 4142

Bravo AF: 0.404

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.45
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs723886; hg19: chr7-68159592;