10-107692722-A-G

Position:

• chr10-107692722-A-G

Variant summary

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

The XR_246185.4(LOC101927573):​n.83+3076A>G 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 0.803 in 152,060 control chromosomes in the GnomAD database, including 50,417 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 0.80 (50417 hom., cov: 31)
• Consequence: LOC101927573 XR_246185.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

LOC101927573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927573	XR_246185.4	n.83+3076A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122085 AN: 151942 Hom.: 50402 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.803 AC: 122142 AN: 152060 Hom.: 50417 Cov.: 31 AF XY: 0.803 AC XY: 59677 AN XY: 74338

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.820

Alfa AF: 0.870 Hom.: 77502

Bravo AF: 0.789

Asia WGS AF: 0.793 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245437; hg19: chr10-109452480;