rs964647

chr6-88226673-A-T

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, non coding transcript 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: ENST00000648572.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648572.1	n.991-48239T>A		intron_variant, non_coding_transcript_variant

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;