rs6965643

Positions:

• chr7-129767724-A-G
• chr7-129767724-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710872.1(ENSG00000286380):​n.432-4318T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,012 control chromosomes in the GnomAD database, including 7,096 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 0.28 (7096 hom., cov: 32)
• Consequence: ENST00000710872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375501	XR_927963.4	n.590+163T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710872.1	n.432-4318T>C		intron_variant, non_coding_transcript_variant
	ENST00000660838.1	n.587+163T>C		intron_variant, non_coding_transcript_variant
	ENST00000704489.2	n.1041+163T>C		intron_variant, non_coding_transcript_variant
	ENST00000704490.1	n.368+163T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42997 AN: 151894 Hom.: 7077 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.283 AC: 43052 AN: 152012 Hom.: 7096 Cov.: 32 AF XY: 0.292 AC XY: 21684 AN XY: 74300

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.280

Alfa AF: 0.225 Hom.: 5530

Bravo AF: 0.294

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6965643; hg19: chr7-129407564;