chr4-161238209-G-T

Variant names:

• chr4-161238209-G-T
• rs10517740
• ENST00000816576.1:n.314+4731C>A

Variant summary

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

The ENST00000816576.1(ENSG00000306264):​n.314+4731C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,622 control chromosomes in the GnomAD database, including 7,338 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 0.30 (7338 hom., cov: 32)
• Consequence: ENSG00000306264 ENST00000816576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

ENSG00000306264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816576.1. 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
	ENSG00000306264	ENST00000816576.1		n.314+4731C>A		intron	N/A
	ENSG00000306264	ENST00000816577.1		n.313+4731C>A		intron	N/A
	ENSG00000306264	ENST00000816578.1		n.339+4731C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45028 AN: 151504 Hom.: 7336 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.297 AC: 45045 AN: 151622 Hom.: 7338 Cov.: 32 AF XY: 0.294 AC XY: 21741 AN XY: 74038

African (AFR) AF: 0.160 AC: 6628 AN: 41452

American (AMR) AF: 0.339 AC: 5140 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3462

East Asian (EAS) AF: 0.284 AC: 1456 AN: 5122

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4816

European-Finnish (FIN) AF: 0.318 AC: 3341 AN: 10516

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24833 AN: 67794

Other (OTH) AF: 0.326 AC: 683 AN: 2092

Alfa AF: 0.178 Hom.: 381

Bravo AF: 0.299

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10517740; hg19: chr4-162159361;