7-127553613-A-G

Variant names:

• chr7-127553613-A-G
• rs11761076
• ENST00000731796.1:n.69+35351T>C

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.69+35351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,082 control chromosomes in the GnomAD database, including 28,877 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 0.61 (28877 hom., cov: 32)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375490	XR_007060511.1	n.92-18382T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.69+35351T>C		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.354+22064T>C		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.161-18382T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92475 AN: 151964 Hom.: 28829 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.609 AC: 92573 AN: 152082 Hom.: 28877 Cov.: 32 AF XY: 0.613 AC XY: 45562 AN XY: 74358

African (AFR) AF: 0.683 AC: 28313 AN: 41484

American (AMR) AF: 0.530 AC: 8098 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3468

East Asian (EAS) AF: 0.880 AC: 4549 AN: 5170

South Asian (SAS) AF: 0.603 AC: 2903 AN: 4816

European-Finnish (FIN) AF: 0.638 AC: 6753 AN: 10584

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38966 AN: 67956

Other (OTH) AF: 0.562 AC: 1186 AN: 2112

Alfa AF: 0.585 Hom.: 4610

Bravo AF: 0.602

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.64
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs11761076; hg19: chr7-127193667;