rs1592365

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-127511269-C-A
• chr7-127511269-C-G
• chr7-127511269-C-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. 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
	ENSG00000295686	ENST00000731796.1		n.70-5903G>T		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.355-25987G>T		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.244-5903G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1592365;

hg19: chr7-127151323;