rs1004561

Variant names:

• chr7-96795015-T-A
• rs1004561
• ENST00000776064.1:n.577+5216T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-96795015-T-A
• chr7-96795015-T-C
• chr7-96795015-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000776064.1(ENSG00000301092):​n.577+5216T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,270 control chromosomes in the GnomAD database, including 195 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 0.043 (195 hom., cov: 33)
• Consequence: ENSG00000301092 ENST00000776064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 5 publications found

Genes affected

ENSG00000301092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776064.1. 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
	ENSG00000301092	ENST00000776064.1		n.577+5216T>A		intron	N/A
	ENSG00000301092	ENST00000776065.1		n.-135T>A		upstream_gene	N/A
	ENSG00000301092	ENST00000776066.1		n.-134T>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6528 AN: 152152 Hom.: 195 Cov.: 33

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0429 AC: 6525 AN: 152270 Hom.: 195 Cov.: 33 AF XY: 0.0427 AC XY: 3181 AN XY: 74452

African (AFR) AF: 0.00999 AC: 415 AN: 41556

American (AMR) AF: 0.0339 AC: 518 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3468

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5178

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4830

European-Finnish (FIN) AF: 0.0570 AC: 605 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0608 AC: 4136 AN: 68010

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0232 Hom.: 13

Bravo AF: 0.0397

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	15
DANN	Benign	0.55
PhyloP100		1.7

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: rs1004561;

hg19: chr7-96424327;