rs7754614

Variant names:

• chr6-9409969-C-T
• rs7754614

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 0.193 in 152,048 control chromosomes in the GnomAD database, including 4,907 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 (4907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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: 0.193 AC: 29354 AN: 151932 Hom.: 4897 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.193 AC: 29418 AN: 152048 Hom.: 4907 Cov.: 32 AF XY: 0.192 AC XY: 14241 AN XY: 74336

African (AFR) AF: 0.458 AC: 18957 AN: 41424

American (AMR) AF: 0.0995 AC: 1521 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0630 AC: 326 AN: 5172

South Asian (SAS) AF: 0.200 AC: 962 AN: 4806

European-Finnish (FIN) AF: 0.0792 AC: 840 AN: 10602

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5868 AN: 67980

Other (OTH) AF: 0.155 AC: 326 AN: 2106

Alfa AF: 0.117 Hom.: 2870

Bravo AF: 0.202

Asia WGS AF: 0.133 AC: 463 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.047
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7754614; hg19: chr6-9410202;