chr6-88226673-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648572.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234426	ENST00000648572.1		n.991-48239T>A		intron	N/A
	ENSG00000298549	ENST00000756364.1		n.310+14895A>T		intron	N/A

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

African (AFR) AF: 0.220 AC: 9133 AN: 41492

American (AMR) AF: 0.0764 AC: 1169 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.102 AC: 490 AN: 4818

European-Finnish (FIN) AF: 0.0527 AC: 559 AN: 10600

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5047 AN: 68012

Other (OTH) AF: 0.109 AC: 230 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.34
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs964647; hg19: chr6-88936392;