chr7-150652849-A-G

Variant names:

• chr7-150652849-A-G
• rs10266069
• XR_007060588.1:n.699-3958T>C

Variant summary

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

The XR_007060588.1(LOC124901774):​n.699-3958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,868 control chromosomes in the GnomAD database, including 25,028 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 0.57 (25028 hom., cov: 32)
• Consequence: LOC124901774 XR_007060588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 8 publications found

Genes affected

LOC124901774 (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 (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901774	XR_007060588.1	n.699-3958T>C		intron_variant	Intron 2 of 2
LOC124901774	XR_007060589.1	n.285-3958T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86362 AN: 151748 Hom.: 25005 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.569 AC: 86440 AN: 151868 Hom.: 25028 Cov.: 32 AF XY: 0.575 AC XY: 42687 AN XY: 74186

African (AFR) AF: 0.649 AC: 26837 AN: 41376

American (AMR) AF: 0.574 AC: 8773 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2652 AN: 5174

South Asian (SAS) AF: 0.645 AC: 3112 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6543 AN: 10528

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35034 AN: 67912

Other (OTH) AF: 0.531 AC: 1118 AN: 2106

Alfa AF: 0.530 Hom.: 65288

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.2
DANN	Benign	0.42
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10266069; hg19: chr7-150349937; COSMIC: COSV107155747;