rs341672

Variant names:

• chr8-2876680-T-C
• rs341672
• ENST00000656456.1:n.45+1192A>G

Variant summary

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

The NR_168441.1(LOC105377785):​n.1166+38916T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,198 control chromosomes in the GnomAD database, including 4,550 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 0.20 (4550 hom., cov: 33)
• Consequence: LOC105377785 NR_168441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 3 publications found

Genes affected

ENSG00000287740 (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 (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_168441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377785	NR_168441.1		n.1166+38916T>C		intron	N/A
	LOC105377785	NR_168442.1		n.1330+29010T>C		intron	N/A
	LOC105377785	NR_168443.1		n.1171+38916T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287740	ENST00000656456.1		n.45+1192A>G		intron	N/A
	ENSG00000253853	ENST00000725259.1		n.1166+38916T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29833 AN: 152080 Hom.: 4540 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.0349

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.196 AC: 29890 AN: 152198 Hom.: 4550 Cov.: 33 AF XY: 0.195 AC XY: 14489 AN XY: 74432

African (AFR) AF: 0.413 AC: 17144 AN: 41482

American (AMR) AF: 0.156 AC: 2386 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1687 AN: 5166

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4824

European-Finnish (FIN) AF: 0.0349 AC: 371 AN: 10626

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5992 AN: 68018

Other (OTH) AF: 0.214 AC: 453 AN: 2114

Alfa AF: 0.134 Hom.: 5739

Bravo AF: 0.215

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.78
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs341672; hg19: chr8-2734202;