rs438895

Positions:

• chr1-8278295-G-A
• chr1-8278295-G-C

Variant summary

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

The XR_007065454.1(LOC124903835):​n.624-16087G>A 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 0.847 in 152,094 control chromosomes in the GnomAD database, including 55,827 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 0.85 (55827 hom., cov: 31)
• Consequence: LOC124903835 XR_007065454.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC124903835 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903835	XR_007065454.1	n.624-16087G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128818 AN: 151976 Hom.: 55826 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.847 AC: 128852 AN: 152094 Hom.: 55827 Cov.: 31 AF XY: 0.850 AC XY: 63199 AN XY: 74362

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.872

Alfa AF: 0.916 Hom.: 107215

Bravo AF: 0.829

Asia WGS AF: 0.901 AC: 3133 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	0.71
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs438895; hg19: chr1-8338355; COSMIC: COSV73920364;