7-128217995-A-T

Variant names:

• chr7-128217995-A-T
• rs11764840
• ENST00000710955.1:n.836-6038A>T

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.836-6038A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,034 control chromosomes in the GnomAD database, including 6,324 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 0.27 (6324 hom., cov: 32)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 4 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.781-6038A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000292309	ENST00000710955.1	n.836-6038A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41288 AN: 151916 Hom.: 6313 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.272 AC: 41334 AN: 152034 Hom.: 6324 Cov.: 32 AF XY: 0.274 AC XY: 20345 AN XY: 74286

African (AFR) AF: 0.146 AC: 6062 AN: 41460

American (AMR) AF: 0.386 AC: 5892 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3472

East Asian (EAS) AF: 0.173 AC: 896 AN: 5180

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4818

European-Finnish (FIN) AF: 0.277 AC: 2918 AN: 10534

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21683 AN: 67982

Other (OTH) AF: 0.263 AC: 555 AN: 2112

Alfa AF: 0.160 Hom.: 330

Bravo AF: 0.275

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.52
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11764840; hg19: chr7-127858048;