6-140841301-C-G

Variant names:

• chr6-140841301-C-G
• rs667816
• XR_428030.5:n.5347G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XR_428030.5(LOC102723724):​n.5347G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.82 (49685 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: LOC102723724 XR_428030.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 2 publications found

Genes affected

LOC102723724 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723724	XR_428030.5	n.5347G>C		non_coding_transcript_exon_variant	Exon 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234147	ENST00000650553.2	n.195-25071G>C		intron_variant	Intron 1 of 4
ENSG00000234147	ENST00000692940.2	n.158-25071G>C		intron_variant	Intron 2 of 2
ENSG00000234147	ENST00000700918.1	n.243-25071G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.816 AC: 120273 AN: 147318 Hom.: 49640 Cov.: 26

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.812

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.816 AC: 120369 AN: 147430 Hom.: 49685 Cov.: 26 AF XY: 0.818 AC XY: 58516 AN XY: 71510

African (AFR) AF: 0.918 AC: 37075 AN: 40398

American (AMR) AF: 0.843 AC: 12364 AN: 14668

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2858 AN: 3436

East Asian (EAS) AF: 0.952 AC: 4721 AN: 4958

South Asian (SAS) AF: 0.872 AC: 4040 AN: 4634

European-Finnish (FIN) AF: 0.702 AC: 6543 AN: 9318

Middle Eastern (MID) AF: 0.746 AC: 209 AN: 280

European-Non Finnish (NFE) AF: 0.753 AC: 50339 AN: 66824

Other (OTH) AF: 0.814 AC: 1648 AN: 2024

Alfa AF: 0.706 Hom.: 1920

Bravo AF: 0.830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.66
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs667816; hg19: chr6-141162438;