rs964647

Variant names:

• chr6-88226673-A-T
• rs964647
• ENST00000648572.1:n.991-48239T>A

Variant summary

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

The ENST00000648572.1(ENSG00000234426):​n.991-48239T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,202 control chromosomes in the GnomAD database, including 1,281 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 0.11 (1281 hom., cov: 31)
• Consequence: ENSG00000234426 ENST00000648572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234426	ENST00000648572.1	n.991-48239T>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16951 AN: 152084 Hom.: 1275 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0742

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.111 AC: 16968 AN: 152202 Hom.: 1281 Cov.: 31 AF XY: 0.110 AC XY: 8156 AN XY: 74424

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.0802

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0742

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0959 Hom.: 106

Bravo AF: 0.115

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964647; hg19: chr6-88936392;