rs1027201

Variant names:

• chr4-44165254-C-T
• rs1027201

Variant summary

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

The variant allele was found at a frequency of 0.272 in 152,002 control chromosomes in the GnomAD database, including 5,965 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 0.27 (5965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 1 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.48 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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41194 AN: 151884 Hom.: 5945 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.272 AC: 41270 AN: 152002 Hom.: 5965 Cov.: 32 AF XY: 0.273 AC XY: 20316 AN XY: 74306

African (AFR) AF: 0.346 AC: 14366 AN: 41462

American (AMR) AF: 0.269 AC: 4116 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2562 AN: 5164

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4818

European-Finnish (FIN) AF: 0.220 AC: 2323 AN: 10546

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14904 AN: 67958

Other (OTH) AF: 0.258 AC: 544 AN: 2106

Alfa AF: 0.238 Hom.: 17959

Bravo AF: 0.283

Asia WGS AF: 0.382 AC: 1326 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	0.67
DANN	Benign	0.58
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1027201; hg19: chr4-44167271;