1-8278295-G-A

Variant names:

• chr1-8278295-G-A
• rs438895
• XR_007065454.1:n.624-16087G>A

Variant summary

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

The XR_007065454.1(LOC124903835):​n.624-16087G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC124903835 (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 = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903835	XR_007065454.1	n.624-16087G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.653 AC: 27068 AN: 41448

American (AMR) AF: 0.820 AC: 12524 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5087 AN: 5162

South Asian (SAS) AF: 0.878 AC: 4231 AN: 4820

European-Finnish (FIN) AF: 0.969 AC: 10262 AN: 10594

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63436 AN: 68014

Other (OTH) AF: 0.872 AC: 1839 AN: 2108

Alfa AF: 0.904 Hom.: 252109

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;