chr6-164164642-G-T

Variant names:

• chr6-164164642-G-T
• rs2764649
• ENST00000850151.1:n.312-73112G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000850151.1(ENSG00000288696):​n.312-73112G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,006 control chromosomes in the GnomAD database, including 9,625 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 0.32 (9625 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 2 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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
ENSG00000288696	ENST00000850151.1	n.312-73112G>T		intron_variant	Intron 3 of 4
ENSG00000288696	ENST00000850152.1	n.372-73112G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48984 AN: 151888 Hom.: 9602 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.323 AC: 49064 AN: 152006 Hom.: 9625 Cov.: 32 AF XY: 0.324 AC XY: 24049 AN XY: 74310

African (AFR) AF: 0.556 AC: 23046 AN: 41426

American (AMR) AF: 0.245 AC: 3744 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1769 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4822

European-Finnish (FIN) AF: 0.232 AC: 2455 AN: 10564

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14311 AN: 67982

Other (OTH) AF: 0.305 AC: 644 AN: 2112

Alfa AF: 0.314 Hom.: 1329

Bravo AF: 0.331

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.43
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs2764649; hg19: chr6-164585674;