rs1417842

Variant names:

• chr6-119668923-A-G
• rs1417842
• ENST00000701940.2:n.325-20102A>G

Variant summary

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

The ENST00000701940.2(ENSG00000287100):​n.325-20102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,018 control chromosomes in the GnomAD database, including 15,734 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 0.44 (15734 hom., cov: 32)
• Consequence: ENSG00000287100 ENST00000701940.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 1 publications found

Genes affected

ENSG00000287100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377975	NR_134600.1	n.252+118528A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287100	ENST00000701940.2	n.325-20102A>G		intron_variant	Intron 3 of 3
ENSG00000287100	ENST00000777516.1	n.319-30418A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67488 AN: 151898 Hom.: 15698 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.445 AC: 67579 AN: 152018 Hom.: 15734 Cov.: 32 AF XY: 0.441 AC XY: 32747 AN XY: 74318

African (AFR) AF: 0.579 AC: 24001 AN: 41436

American (AMR) AF: 0.475 AC: 7251 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1392 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2888 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1622 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3296 AN: 10566

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25676 AN: 67970

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.401 Hom.: 44878

Bravo AF: 0.465

Asia WGS AF: 0.425 AC: 1471 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1417842; hg19: chr6-119990080;