rs10937751

chr4-6710329-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741568.3(LOC105378240):n.121+274A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,986 control chromosomes in the GnomAD database, including 40,726 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 0.73 (40726 hom., cov: 31)
• Consequence: LOC105378240 XR_001741568.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

LOC105378240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378240	XR_001741568.3	n.121+274A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.731 AC: 110995 AN: 151868 Hom.: 40696 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.731 AC: 111080 AN: 151986 Hom.: 40726 Cov.: 31 AF XY: 0.732 AC XY: 54372 AN XY: 74280

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.723

Alfa AF: 0.719 Hom.: 25499

Bravo AF: 0.730

Asia WGS AF: 0.611 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937751; hg19: chr4-6712056;