rs6969537

Variant names:

• chr7-55014725-A-G
• rs6969537
• ENST00000836965.1:n.298+1230A>G

Variant summary

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

The ENST00000836965.1(ENSG00000308870):​n.298+1230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,128 control chromosomes in the GnomAD database, including 55,417 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 0.85 (55417 hom., cov: 31)
• Consequence: ENSG00000308870 ENST00000836965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 14 publications found

Genes affected

ENSG00000308870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375284	XR_007060329.1	n.2362+1836T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308870	ENST00000836965.1	n.298+1230A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129693 AN: 152010 Hom.: 55391 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.853 AC: 129774 AN: 152128 Hom.: 55417 Cov.: 31 AF XY: 0.852 AC XY: 63354 AN XY: 74366

African (AFR) AF: 0.841 AC: 34872 AN: 41480

American (AMR) AF: 0.810 AC: 12352 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5160 AN: 5172

South Asian (SAS) AF: 0.951 AC: 4588 AN: 4826

European-Finnish (FIN) AF: 0.825 AC: 8730 AN: 10586

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57978 AN: 68014

Other (OTH) AF: 0.876 AC: 1851 AN: 2114

Alfa AF: 0.857 Hom.: 181240

Bravo AF: 0.851

Asia WGS AF: 0.949 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.35
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6969537; hg19: chr7-55082418;