rs628926

chr9-117839528-T-C

Variant summary

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

The ENST00000697639.1(ENSG00000284977):n.963-8537T>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 0.67 in 152,066 control chromosomes in the GnomAD database, including 35,093 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 0.67 (35093 hom., cov: 32)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376244	XR_007061905.1	n.2991-8537T>C		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061906.1	n.2408-8537T>C		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061907.1	n.2147-8537T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.963-8537T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101720 AN: 151946 Hom.: 35049 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.670 AC: 101820 AN: 152066 Hom.: 35093 Cov.: 32 AF XY: 0.664 AC XY: 49330 AN XY: 74308

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.674

Alfa AF: 0.648 Hom.: 4011

Bravo AF: 0.686

Asia WGS AF: 0.576 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.10
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs628926; hg19: chr9-120601806; COSMIC: COSV69947130; COSMIC: COSV69947130;