chr6-90374161-C-G

Variant names:

• chr6-90374161-C-G
• rs10498968
• ENST00000741971.1:n.194+3197C>G

Variant summary

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

The ENST00000741971.1(ENSG00000296783):​n.194+3197C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,058 control chromosomes in the GnomAD database, including 3,548 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 0.21 (3548 hom., cov: 32)
• Consequence: ENSG00000296783 ENST00000741971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 2 publications found

Genes affected

ENSG00000296783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741971.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296783	ENST00000741971.1		n.194+3197C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31712 AN: 151940 Hom.: 3537 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.209 AC: 31740 AN: 152058 Hom.: 3548 Cov.: 32 AF XY: 0.204 AC XY: 15191 AN XY: 74330

African (AFR) AF: 0.182 AC: 7532 AN: 41456

American (AMR) AF: 0.166 AC: 2530 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3466

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5176

South Asian (SAS) AF: 0.252 AC: 1215 AN: 4812

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10586

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16622 AN: 67968

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.223 Hom.: 486

Bravo AF: 0.204

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.68
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10498968; hg19: chr6-91083880;