rs11665698

Variant names:

• chr19-50851155-A-C
• rs11665698
• ENST00000598079.1:n.*66A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-50851155-A-C
• chr19-50851155-A-G

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.*66A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,010 control chromosomes in the GnomAD database, including 32,197 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 0.65 (32195 hom., cov: 32)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: ENSG00000267968 ENST00000598079.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 4 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.*12A>C		downstream_gene_variant
LOC105372441	NR_131205.1	n.*12A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.*66A>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98237 AN: 151882 Hom.: 32179 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.625

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 2 AF XY: 0.500 AC XY: 3 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.647 AC: 98294 AN: 152000 Hom.: 32195 Cov.: 32 AF XY: 0.648 AC XY: 48187 AN XY: 74312

African (AFR) AF: 0.580 AC: 24034 AN: 41414

American (AMR) AF: 0.665 AC: 10161 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2104 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2895 AN: 5150

South Asian (SAS) AF: 0.480 AC: 2308 AN: 4810

European-Finnish (FIN) AF: 0.813 AC: 8612 AN: 10594

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46087 AN: 67966

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

Alfa AF: 0.658 Hom.: 25773

Bravo AF: 0.633

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11665698; hg19: chr19-51354411;