rs6948646

Variant names:

• chr7-153248199-A-G
• rs6948646
• XR_007060599.1:n.2404+3633A>G

Variant summary

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

The XR_007060599.1(LOC102723686):​n.2404+3633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,074 control chromosomes in the GnomAD database, including 22,788 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 0.51 (22788 hom., cov: 32)
• Consequence: LOC102723686 XR_007060599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 5 publications found

Genes affected

LOC102723686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77996 AN: 151950 Hom.: 22789 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.513 AC: 78007 AN: 152074 Hom.: 22788 Cov.: 32 AF XY: 0.515 AC XY: 38262 AN XY: 74332

African (AFR) AF: 0.216 AC: 8944 AN: 41500

American (AMR) AF: 0.584 AC: 8914 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5162

South Asian (SAS) AF: 0.567 AC: 2732 AN: 4818

European-Finnish (FIN) AF: 0.657 AC: 6941 AN: 10568

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43899 AN: 67968

Other (OTH) AF: 0.546 AC: 1155 AN: 2114

Alfa AF: 0.601 Hom.: 15920

Bravo AF: 0.494

Asia WGS AF: 0.506 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.4
DANN	Benign	0.60
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6948646; hg19: chr7-152945284;