rs6702835

Variant names:

• chr1-173489961-G-A
• rs6702835
• XR_007066738.1:n.2846C>T

Variant summary

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

The XR_007066738.1(LOC124904456):​n.2846C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,898 control chromosomes in the GnomAD database, including 11,907 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 0.35 (11907 hom., cov: 31)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 5 publications found

Genes affected

LOC124904456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904456	XR_007066738.1	n.2846C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53763 AN: 151780 Hom.: 11868 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.355 AC: 53867 AN: 151898 Hom.: 11907 Cov.: 31 AF XY: 0.352 AC XY: 26116 AN XY: 74244

African (AFR) AF: 0.609 AC: 25238 AN: 41422

American (AMR) AF: 0.257 AC: 3928 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3075 AN: 5156

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4816

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16303 AN: 67920

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.313 Hom.: 4799

Bravo AF: 0.372

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.71
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6702835; hg19: chr1-173459100;