rs1150790

Variant names:

• chr6-37212747-A-C
• rs1150790
• NM_001395378.1:c.223T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-37212747-A-C
• chr6-37212747-A-G
• chr6-37212747-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001395378.1(TMEM217B):​c.223T>G​(p.Phe75Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 6/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000019 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TMEM217B NM_001395378.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 11 publications found

Genes affected

TMEM217B (HGNC:55922): (transmembrane protein 217B)

TMEM217 (HGNC:21238): (transmembrane protein 217) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM217B	NM_001395378.1	c.223T>G	p.Phe75Val	missense_variant	Exon 2 of 2	ENST00000497775.2	NP_001382307.1
TMEM217	NM_001286401.2	c.*219T>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000651039.2	NP_001273330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM217B	ENST00000497775.2	c.223T>G	p.Phe75Val	missense_variant	Exon 2 of 2	2	NM_001395378.1	ENSP00000499172.1
TMEM217	ENST00000651039.2	c.*219T>G		3_prime_UTR_variant	Exon 3 of 3		NM_001286401.2	ENSP00000499204.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000188 AC: 1 AN: 531328 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 288290

African (AFR) AF: 0.00 AC: 0 AN: 15298

American (AMR) AF: 0.0000295 AC: 1 AN: 33884

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19348

East Asian (EAS) AF: 0.00 AC: 0 AN: 30402

South Asian (SAS) AF: 0.00 AC: 0 AN: 61754

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33380

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3946

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 304092

Other (OTH) AF: 0.00 AC: 0 AN: 29224

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.58
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1150790; hg19: chr6-37180523;