7-134644207-C-G

Variant names:

• chr7-134644207-C-G
• rs3757397
• XR_007060537.1:n.29222-24259G>C

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-24259G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,962 control chromosomes in the GnomAD database, including 26,829 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 0.58 (26829 hom., cov: 31)
• Consequence: LOC124901750 XR_007060537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 2 publications found

Genes affected

LOC124901750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-24259G>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88509 AN: 151844 Hom.: 26805 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.583 AC: 88591 AN: 151962 Hom.: 26829 Cov.: 31 AF XY: 0.589 AC XY: 43764 AN XY: 74260

African (AFR) AF: 0.711 AC: 29479 AN: 41474

American (AMR) AF: 0.563 AC: 8591 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4579 AN: 5154

South Asian (SAS) AF: 0.717 AC: 3454 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5593 AN: 10520

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33353 AN: 67948

Other (OTH) AF: 0.553 AC: 1165 AN: 2108

Alfa AF: 0.524 Hom.: 2692

Bravo AF: 0.589

Asia WGS AF: 0.763 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.38
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3757397; hg19: chr7-134328959;