7-7335192-T-C

Variant names:

• chr7-7335192-T-C
• rs6955140
• XR_002956539.2:n.442-41369T>C

Variant summary

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

The XR_002956539.2(LOC107986764):​n.442-41369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,022 control chromosomes in the GnomAD database, including 46,884 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 0.78 (46884 hom., cov: 31)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

Genes affected

LOC107986764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119141 AN: 151904 Hom.: 46843 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.784 AC: 119236 AN: 152022 Hom.: 46884 Cov.: 31 AF XY: 0.790 AC XY: 58670 AN XY: 74276

African (AFR) AF: 0.748 AC: 31023 AN: 41454

American (AMR) AF: 0.811 AC: 12387 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2685 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4534 AN: 5158

South Asian (SAS) AF: 0.829 AC: 3989 AN: 4814

European-Finnish (FIN) AF: 0.819 AC: 8660 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53338 AN: 67960

Other (OTH) AF: 0.779 AC: 1644 AN: 2110

Alfa AF: 0.785 Hom.: 10755

Bravo AF: 0.781

Asia WGS AF: 0.859 AC: 2988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.46
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs6955140; hg19: chr7-7374823;