rs6960395

Variant names:

• chr7-97193557-G-A
• rs6960395
• XR_007060445.1:n.132-13208C>T

Variant summary

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

The XR_007060445.1(LOC124901704):​n.132-13208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,032 control chromosomes in the GnomAD database, including 38,364 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 0.71 (38364 hom., cov: 33)
• Consequence: LOC124901704 XR_007060445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 0 publications found

Genes affected

LOC124901704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.708 AC: 107518 AN: 151914 Hom.: 38328 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.708 AC: 107605 AN: 152032 Hom.: 38364 Cov.: 33 AF XY: 0.710 AC XY: 52791 AN XY: 74320

African (AFR) AF: 0.706 AC: 29281 AN: 41448

American (AMR) AF: 0.757 AC: 11565 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3472

East Asian (EAS) AF: 0.873 AC: 4520 AN: 5178

South Asian (SAS) AF: 0.804 AC: 3880 AN: 4826

European-Finnish (FIN) AF: 0.636 AC: 6700 AN: 10540

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46714 AN: 67972

Other (OTH) AF: 0.718 AC: 1517 AN: 2112

Alfa AF: 0.705 Hom.: 14038

Bravo AF: 0.716

Asia WGS AF: 0.808 AC: 2802 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs6960395; hg19: chr7-96822869;