rs1350666

Variant names:

• chr4-74358873-T-C
• rs1350666
• ENST00000805841.1:n.191+6278A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-74358873-T-C
• chr4-74358873-T-G

Variant summary

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

The NR_188415.1(LOC105377276):​n.191+6278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,904 control chromosomes in the GnomAD database, including 34,354 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 0.66 (34354 hom., cov: 32)
• Consequence: LOC105377276 NR_188415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 20 publications found

Genes affected

ENSG00000304732 (HGNC:58817):

LOC105377276 (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 (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188415.1. 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
	LOC105377276	NR_188415.1		n.191+6278A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.191+6278A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100334 AN: 151786 Hom.: 34342 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.661 AC: 100381 AN: 151904 Hom.: 34354 Cov.: 32 AF XY: 0.660 AC XY: 48963 AN XY: 74238

African (AFR) AF: 0.484 AC: 20083 AN: 41458

American (AMR) AF: 0.747 AC: 11402 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2649 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2683 AN: 5154

South Asian (SAS) AF: 0.572 AC: 2752 AN: 4814

European-Finnish (FIN) AF: 0.735 AC: 7760 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50555 AN: 67884

Other (OTH) AF: 0.702 AC: 1479 AN: 2106

Alfa AF: 0.718 Hom.: 165749

Bravo AF: 0.656

Asia WGS AF: 0.529 AC: 1835 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1350666; hg19: chr4-75224590;