rs1611192

Variant names:

• chr6-29804102-A-G
• rs1611192
• ENST00000849927.1:n.191+2186T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-29804102-A-G
• chr6-29804102-A-T

Variant summary

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

The ENST00000849927.1(HLA-F-AS1):​n.191+2186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 288,962 control chromosomes in the GnomAD database, including 6,179 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 0.22 (3634 hom., cov: 32)
  • Exomes 𝑓: 0.18 (2545 hom.)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 15 publications found

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

HLA-V (HGNC:):

RPL7AP7 (HGNC:21395): (ribosomal protein L7a pseudogene 7)

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 (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000849927.1	n.191+2186T>C		intron_variant	Intron 2 of 3
HLA-V	ENST00000850477.1	n.364-887A>G		intron_variant	Intron 2 of 2
HLA-V	ENST00000850478.1	n.335-887A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32953 AN: 152056 Hom.: 3635 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.176 AC: 24032 AN: 136788 Hom.: 2545 AF XY: 0.179 AC XY: 12807 AN XY: 71608

African (AFR) AF: 0.197 AC: 581 AN: 2944

American (AMR) AF: 0.193 AC: 1058 AN: 5488

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 773 AN: 4436

East Asian (EAS) AF: 0.0521 AC: 472 AN: 9054

South Asian (SAS) AF: 0.214 AC: 1546 AN: 7214

European-Finnish (FIN) AF: 0.144 AC: 1222 AN: 8478

Middle Eastern (MID) AF: 0.225 AC: 136 AN: 604

European-Non Finnish (NFE) AF: 0.186 AC: 16627 AN: 89632

Other (OTH) AF: 0.181 AC: 1617 AN: 8938

GnomAD4 genome AF: 0.217 AC: 32950 AN: 152174 Hom.: 3634 Cov.: 32 AF XY: 0.211 AC XY: 15715 AN XY: 74398

African (AFR) AF: 0.215 AC: 8921 AN: 41486

American (AMR) AF: 0.216 AC: 3306 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3468

East Asian (EAS) AF: 0.0676 AC: 351 AN: 5190

South Asian (SAS) AF: 0.205 AC: 989 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1740 AN: 10588

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16214 AN: 68014

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.233 Hom.: 5992

Bravo AF: 0.222

Asia WGS AF: 0.132 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1611192; hg19: chr6-29771879;