ENST00000765264.1:n.227-4918A>G

Variant names:

• chr7-135755167-A-G
• rs10257539
• ENST00000765264.1:n.227-4918A>G

Variant summary

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

The ENST00000765264.1(ENSG00000299635):​n.227-4918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,162 control chromosomes in the GnomAD database, including 42,323 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 0.74 (42323 hom., cov: 32)
• Consequence: ENSG00000299635 ENST00000765264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 0 publications found

Genes affected

ENSG00000299635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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
ENSG00000299635	ENST00000765264.1	n.227-4918A>G		intron_variant	Intron 2 of 3
ENSG00000299635	ENST00000765265.1	n.346-4918A>G		intron_variant	Intron 1 of 2
ENSG00000299635	ENST00000765266.1	n.80-4918A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112365 AN: 152044 Hom.: 42249 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.739 AC: 112498 AN: 152162 Hom.: 42323 Cov.: 32 AF XY: 0.741 AC XY: 55146 AN XY: 74390

African (AFR) AF: 0.891 AC: 37006 AN: 41528

American (AMR) AF: 0.735 AC: 11227 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3472

East Asian (EAS) AF: 0.722 AC: 3736 AN: 5176

South Asian (SAS) AF: 0.704 AC: 3392 AN: 4816

European-Finnish (FIN) AF: 0.732 AC: 7745 AN: 10582

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44863 AN: 67984

Other (OTH) AF: 0.737 AC: 1560 AN: 2116

Alfa AF: 0.681 Hom.: 150666

Bravo AF: 0.748

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10257539; hg19: chr7-135439915;