7-37604441-A-T

Variant names:

• chr7-37604441-A-T
• rs10488659
• ENST00000764643.1:n.174-3296T>A

Variant summary

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

The ENST00000764643.1(ENSG00000299559):​n.174-3296T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 152,248 control chromosomes in the GnomAD database, including 418 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 0.046 (418 hom., cov: 32)
• Consequence: ENSG00000299559 ENST00000764643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 1 publications found

Genes affected

ENSG00000299559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764643.1. 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
	ENSG00000299559	ENST00000764643.1		n.174-3296T>A		intron	N/A
	ENSG00000299559	ENST00000764644.1		n.168-3293T>A		intron	N/A
	ENSG00000299559	ENST00000764645.1		n.395-3296T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6970 AN: 152130 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.00924

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0457 AC: 6962 AN: 152248 Hom.: 418 Cov.: 32 AF XY: 0.0505 AC XY: 3762 AN XY: 74428

African (AFR) AF: 0.00922 AC: 383 AN: 41558

American (AMR) AF: 0.0334 AC: 510 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5174

South Asian (SAS) AF: 0.178 AC: 859 AN: 4816

European-Finnish (FIN) AF: 0.0830 AC: 881 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2620 AN: 68016

Other (OTH) AF: 0.0346 AC: 73 AN: 2110

Alfa AF: 0.0136 Hom.: 8

Bravo AF: 0.0406

Asia WGS AF: 0.209 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		-0.36

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: rs10488659;

hg19: chr7-37644044;