rs11191416

Variant names:

• chr10-102845159-T-G
• rs11191416
• ENST00000744031.1:n.1265A>C

Variant summary

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

The ENST00000744031.1(ENSG00000282772):​n.1265A>C 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 0.117 in 230,918 control chromosomes in the GnomAD database, including 2,134 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 0.11 (1139 hom., cov: 32)
  • Exomes 𝑓: 0.14 (995 hom.)
• Consequence: ENSG00000282772 ENST00000744031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• Publications: 53 publications found

Genes affected

ENSG00000282772 (HGNC:):

PFN1P11 (HGNC:42994): (profilin 1 pseudogene 11)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744031.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282772	ENST00000744031.1		n.1265A>C		non_coding_transcript_exon	Exon 2 of 2
	PFN1P11	ENST00000445829.1	TSL:6	n.290+25A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16279 AN: 152042 Hom.: 1135 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.115

GnomAD4 exome AF: 0.137 AC: 10816 AN: 78758 Hom.: 995 Cov.: 0 AF XY: 0.135 AC XY: 6151 AN XY: 45590

African (AFR) AF: 0.0775 AC: 157 AN: 2026

American (AMR) AF: 0.226 AC: 1931 AN: 8550

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 92 AN: 1086

East Asian (EAS) AF: 0.342 AC: 1505 AN: 4402

South Asian (SAS) AF: 0.235 AC: 1890 AN: 8048

European-Finnish (FIN) AF: 0.0897 AC: 980 AN: 10926

Middle Eastern (MID) AF: 0.0950 AC: 79 AN: 832

European-Non Finnish (NFE) AF: 0.0968 AC: 3847 AN: 39744

Other (OTH) AF: 0.107 AC: 335 AN: 3144

GnomAD4 genome AF: 0.107 AC: 16298 AN: 152160 Hom.: 1139 Cov.: 32 AF XY: 0.110 AC XY: 8173 AN XY: 74392

African (AFR) AF: 0.0715 AC: 2968 AN: 41524

American (AMR) AF: 0.146 AC: 2228 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 288 AN: 3460

East Asian (EAS) AF: 0.342 AC: 1767 AN: 5170

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4816

European-Finnish (FIN) AF: 0.0874 AC: 927 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6753 AN: 67982

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.104 Hom.: 277

Bravo AF: 0.111

Asia WGS AF: 0.239 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.52
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs11191416; hg19: chr10-104604916;