chr16-56663179-G-T

Variant names:

• chr16-56663179-G-T
• rs7194895
• ENST00000849089.1:n.150G>T

Variant summary

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

The ENST00000849089.1(ENSG00000310325):​n.150G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,004 control chromosomes in the GnomAD database, including 9,027 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 0.34 (9027 hom., cov: 32)
• Consequence: ENSG00000310325 ENST00000849089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 12 publications found

Genes affected

ENSG00000310325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849089.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310325	ENST00000849089.1		n.150G>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000310325	ENST00000849090.1		n.100G>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000310278	ENST00000848704.1		n.84+25C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51733 AN: 151884 Hom.: 9015 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.341 AC: 51770 AN: 152004 Hom.: 9027 Cov.: 32 AF XY: 0.343 AC XY: 25469 AN XY: 74316

African (AFR) AF: 0.291 AC: 12089 AN: 41504

American (AMR) AF: 0.403 AC: 6150 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1671 AN: 5148

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4818

European-Finnish (FIN) AF: 0.418 AC: 4418 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24274 AN: 67902

Other (OTH) AF: 0.326 AC: 690 AN: 2114

Alfa AF: 0.323 Hom.: 3949

Bravo AF: 0.339

Asia WGS AF: 0.313 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7194895; hg19: chr16-56697091; COSMIC: COSV57622462;