7-127511269-C-A

Variant names:

• chr7-127511269-C-A
• rs1592365
• ENST00000731796.1:n.70-5903G>T

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-5903G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,972 control chromosomes in the GnomAD database, including 13,396 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 0.39 (13396 hom., cov: 32)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 3 publications found

Genes affected

ENSG00000295686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2292-2031G>T		intron_variant	Intron 2 of 4
LOC105375490	XR_001745352.2	n.494-2031G>T		intron_variant	Intron 3 of 5
LOC105375490	XR_007060511.1	n.175-2031G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-5903G>T		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.355-25987G>T		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.244-5903G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58624 AN: 151850 Hom.: 13380 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.386 AC: 58647 AN: 151972 Hom.: 13396 Cov.: 32 AF XY: 0.394 AC XY: 29246 AN XY: 74282

African (AFR) AF: 0.156 AC: 6480 AN: 41466

American (AMR) AF: 0.409 AC: 6246 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1026 AN: 3460

East Asian (EAS) AF: 0.802 AC: 4122 AN: 5142

South Asian (SAS) AF: 0.479 AC: 2303 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5380 AN: 10564

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31800 AN: 67938

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.426 Hom.: 3049

Bravo AF: 0.368

Asia WGS AF: 0.588 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.8
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1592365; hg19: chr7-127151323;