chr9-121370602-A-G

Variant names:

• chr9-121370602-A-G
• rs1771889
• ENST00000637541.1:n.112A>G

Variant summary

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

The ENST00000637541.1(ENSG00000227355):​n.112A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 188,048 control chromosomes in the GnomAD database, including 16,215 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 0.41 (13595 hom., cov: 33)
  • Exomes 𝑓: 0.36 (2620 hom.)
• Consequence: ENSG00000227355 ENST00000637541.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 8 publications found

Genes affected

ENSG00000227355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723324	NR_187150.1	n.88A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC102723324	NR_187151.1	n.88A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC102723324	NR_187152.1	n.88A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227355	ENST00000637541.1	n.112A>G		non_coding_transcript_exon_variant	Exon 1 of 3	3
ENSG00000227355	ENST00000685727.2	n.159A>G		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000227355	ENST00000688457.2	n.89A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62699 AN: 151990 Hom.: 13561 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 0.360 AC: 12929 AN: 35940 Hom.: 2620 Cov.: 0 AF XY: 0.350 AC XY: 6688 AN XY: 19108

African (AFR) AF: 0.508 AC: 843 AN: 1658

American (AMR) AF: 0.248 AC: 582 AN: 2344

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 588 AN: 1190

East Asian (EAS) AF: 0.102 AC: 268 AN: 2640

South Asian (SAS) AF: 0.211 AC: 650 AN: 3086

European-Finnish (FIN) AF: 0.325 AC: 481 AN: 1480

Middle Eastern (MID) AF: 0.449 AC: 71 AN: 158

European-Non Finnish (NFE) AF: 0.404 AC: 8653 AN: 21396

Other (OTH) AF: 0.399 AC: 793 AN: 1988

GnomAD4 genome AF: 0.413 AC: 62779 AN: 152108 Hom.: 13595 Cov.: 33 AF XY: 0.404 AC XY: 30032 AN XY: 74364

African (AFR) AF: 0.500 AC: 20746 AN: 41488

American (AMR) AF: 0.333 AC: 5086 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3472

East Asian (EAS) AF: 0.128 AC: 658 AN: 5158

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4828

European-Finnish (FIN) AF: 0.345 AC: 3655 AN: 10596

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28328 AN: 67952

Other (OTH) AF: 0.403 AC: 851 AN: 2112

Alfa AF: 0.416 Hom.: 2776

Bravo AF: 0.417

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.65
PhyloP100		0.42
PromoterAI		0.0084	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1771889; hg19: chr9-124132880; COSMIC: COSV54417771;